NetLogo Web: neuronal membrane_one functional channel

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model speed ticks: 0

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Channel Properties

Command Center NetLogo Code

x
 
breed [particles particle]
breed [ion-channels ion-channel]
​
particles-own [my-position charge]
​
globals [
  inside-cell
  outside-cell
  membrane-patches
]
​
ion-channels-own [my-type]
​
to setup
  clear-all
​
   ; add sodium ions inside
​
    ask patches with [pxcor < -2] [
      if random 100 < 10 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color red
          fd random-float 1
          set my-position "inside"
          set charge "positive"
        ]
      ]
    ]
​
  ; add sodium ions outside
​
    ask patches with [pxcor > 2] [
      if random 100 < 98 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color red
          fd random-float 1
          set my-position "outside"
          set charge "positive"
        ]
      ]
    ]
​
​
  ; add chloride ions inside
​
    ask patches with [pxcor < -2] [
      if random 100 < 9 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color green
          fd random-float 1
          set my-position "inside"
          set charge "negative"
        ]
      ]
    ]
​
  ; add chloride ions outside
​
    ask patches with [pxcor > 2] [
      if random 100 < 100 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color green
          fd random-float 1
          set my-position "outside"
         set charge "negative"
        ]
      ]
    ]
​
  ; add potassium ions inside
​
    ask patches with [pxcor < -2] [
      if random 100 < 83 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color yellow
          fd random-float 1
          set my-position "inside"
          set charge "positive"
        ]
      ]
    ]
​
  ; add potassium ions outside
​
   ask patches with [pxcor > 2] [
      if random 100 < 3 [
        sprout-particles 1 [
          set shape "circle"
          set size 0.5
          set color yellow
          fd random-float 1
          set my-position "outside"
          set charge "positive"
        ]
      ]
   ]
​
  ; make chambers
​
  ask patches with [pxcor < 2 and pxcor > -2] [set pcolor blue]
​
  ; patches that can have ion-channels
  set membrane-patches patches with [pxcor = 0 and (pycor < max-pycor - 1) and (pycor > min-pycor + 1)]
​
​
  ; make sodium channels
​
  ask n-of 5 membrane-patches [sprout-ion-channels 1 [
    set size 4
    set heading 180
    set my-type "Na-channel"
    set color red
    set shape "open Ion Channel"
    ]
  ]
  
  
  ; make choloride channels
​
  ask n-of 5 membrane-patches with [count ion-channels-here = 0 ] [sprout-ion-channels 1 [
    set size 4
    set heading 180
    set my-type "Cl-channel"
    set color green
    set shape "open Ion Channel"
    ]
  ]
  
   ; make potassium channels
​
  ask n-of 5 membrane-patches with [count ion-channels-here = 0 ] [sprout-ion-channels 1 [
    set size 4
    set heading 180
    set my-type "K-channel"
    set color yellow
    set shape "open Ion Channel"
    ]
  ]
​
  set inside-cell patches with [pxcor < 0 and pcolor = black]
  set outside-cell patches with [pxcor > 0 and pcolor = black]
​
  reset-ticks
​
end
​
to random-walk
​
  ; take a step forward through fractional distance less than 1
  fd random-float 1
​
  ;randomize direction (heading) for the next step
  rt random 360
​
end
​
​
to go
​
  ifelse trace-path? [
    ask particles [pen-down]
  ]
  [
    ask particles [pen-up]
  ]
​
​
​
​
    ask particles [
    ; if you are near a blue wall or an edge , turn back, else do the random walk
​
    if my-position = "inside" [
​
    if patch-ahead 1 = nobody [
      set heading 90
      fd 1
    ]
​
    if [pcolor] of patch-ahead 1 = blue [
      set heading 270
      fd 1
    ]
​
     ]
​
​
​
    if my-position = "outside" [
​
    if patch-ahead 1 = nobody [
      set heading 270
      fd 1
    ]
​
    if [pcolor] of patch-ahead 1 = blue [
      set heading 90
      fd 1
    ]
​
    ]
​
    random-walk
​
   ; additional movement because of the charges
​
   if strength-of-the-field > 0 [
​
      if charge = "positive" [
       if (xcor + strength-of-the-field) < max-pxcor [          ; to make sure that the particle does not move beyod the edge of the world
       set xcor  (xcor + strength-of-the-field)
       ]
     ]
​
      if charge = "negative" [
       if (xcor - strength-of-the-field) > min-pxcor [          ; to make sure that the particle does not move beyod the edge of the world
       set xcor  (xcor - strength-of-the-field)
       ]
      ]
    ]
​
   if strength-of-the-field < 0 [
​
      if charge = "positive" [
       if (xcor + strength-of-the-field) > min-pxcor [          ; to make sure that the particle does not move beyod the edge of the world
       set xcor  (xcor + strength-of-the-field)
       ]
     ]
​
      if charge = "negative" [
       if (xcor - strength-of-the-field) < max-pxcor [          ; to make sure that the particle does not move beyod the edge of the world
       set xcor  (xcor - strength-of-the-field)
       ]
      ]
    ]
​
​
  ]
  
  
  ; transport Na outside to inside and inside to outside
​
  ; inside to outside
  ask ion-channels with [my-type = "Na-channel"]
​
  [
    if any? particles in-radius 3 with [my-position = "inside" and color = red]
​
    [
      if random-float 1 < Na-transportation-probability
      [
        let destination-patches (outside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "inside" and color = red ]
        [
          move-to one-of destination-patches
          set my-position "outside"
        ]
      ]
    ]
​
    ; outside to inside
​
    if any? particles in-radius 3 with [my-position = "outside" and color = red]
​
    [
      if random-float 1 < Na-transportation-probability
      [
        let destination-patches (inside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "outside" and color = red ]
        [
          move-to one-of destination-patches
          set my-position "inside"
        ]
      ]
    ]
  ] 
    
  ; transport Cl outside to inside and inside to outside
​
  ; inside to outside
  ask ion-channels with [my-type = "Cl-channel"]
​
  [
    if any? particles in-radius 3 with [my-position = "inside" and color = green]
​
    [
      if random-float 1 < Cl-transportation-probability
      [
        let destination-patches (outside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "inside" and color = green ]
        [
          move-to one-of destination-patches
          set my-position "outside"
        ]
      ]
    ]
​
    ; outside to inside
​
    if any? particles in-radius 3 with [my-position = "outside" and color = green]
​
    [
      if random-float 1 < Cl-transportation-probability
      [
        let destination-patches (inside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "outside" and color = green ]
        [
          move-to one-of destination-patches
          set my-position "inside"
        ]
      ]
    ]
​
  ]
  
   ; transport K outside to inside and inside to outside
​
  ; inside to outside
  ask ion-channels with [my-type = "K-channel"]
​
  [
    if any? particles in-radius 3 with [my-position = "inside" and color = yellow]
​
    [
      if random-float 1 < Cl-transportation-probability
      [
        let destination-patches (outside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "inside" and color = yellow ]
        [
          move-to one-of destination-patches
          set my-position "outside"
        ]
      ]
    ]
​
    ; outside to inside
​
    if any? particles in-radius 3 with [my-position = "outside" and color = yellow]
​
    [
      if random-float 1 < Cl-transportation-probability
      [
        let destination-patches (inside-cell in-radius 2)
        ask one-of particles in-radius 3 with [my-position = "outside" and color = yellow ]
        [
          move-to one-of destination-patches
          set my-position "inside"
        ]
      ]
    ]
​
  ]
​
​
  tick
​
end

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neuronal membrane_all channels